So I ran across something today that I hadn’t seen before on my 64gb Nexus 6. When I upgraded to Marshmallow it was only recognizing 32gb of space (basically showing me 23gb free).
A quick search on Google turned up the following tidbit of information:
If you have TWRP installed, or if you choose to install it after you discover this problem, then you have an option that will preserve your data: use the new “resize partition” function within recovery.
Boot to TWRP (version 126.96.36.199 or higher)
Choose “Wipe” button (do not slide yet!!) then “Advanced Wipe” button.
Select the Data partition, then “Repair or Change File System” button.
Choose the Resize button.
Now you can slide to confirm, and it will expand the partition to it’s full potential, without disturbing the data.
It’s in several places, reddit and XDA included so not going to relink it. Apparently this was a bug with both Lollipop and Marshmallow. The above instructions, if you follow them correctly, will leave your data untouched. I have been running my phone unrooted and stock recently but it’s easy enough to load TWRP on temporarily and then go back to stock recovery.